Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate Echvi_2458 Echvi_2458 histidinol-phosphate aminotransferase
Query= metacyc::BSU22620-MONOMER (360 letters) >FitnessBrowser__Cola:Echvi_2458 Length = 354 Score = 187 bits (476), Expect = 3e-52 Identities = 123/365 (33%), Positives = 198/365 (54%), Gaps = 31/365 (8%) Query: 3 IKEHLKQLKPYQPGKPIEAVKSEYGLDKVVKLASNENPYGCSEAAKEALHHEIQQLALYP 62 ++ H+ QLKPY + + EY + V L +NENP+G A + YP Sbjct: 9 LRPHIAQLKPYS------SARDEYTGKEGVFLDANENPFGSITA---------ESFNRYP 53 Query: 63 DGYSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLND-KTNTVTAAPTFPQYKHN 121 D Y AL+ ++S V + GNGSDE I ++ RAF K N + PT+ Y+ + Sbjct: 54 DPYQHALKEKISAIKQVPVEQIFIGNGSDEAIDLLMRAFCRPGKDNIIILPPTYGMYEVS 113 Query: 122 AVIEGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERV 181 A I ++ + L D DA+LEA+DE T++++ICSPNNP+G ++L + V Sbjct: 114 ADINDISIKRVNLSADFQLRPDAILEAVDENTKIIFICSPNNPSGNKVRRKDILKII--V 171 Query: 182 PSRVLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENL 241 LVV+DEAY ++ D P L ++ NL++++TFSKA+GLAALR+G A + Sbjct: 172 GFDGLVVVDEAYIDF---SDEPSFTAELPQHPNLLVMQTFSKAWGLAALRLGMAFASLPI 228 Query: 242 IRQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQ----YYDFAKTHGL-K 296 IR + + P+N S L Q + AL D + + V++ LQ+ + +K G+ K Sbjct: 229 IRILNKIKPPYNISGLTQETVLKALQDTSKMKQMVKEM---LQERDYLLHALSKMDGIKK 285 Query: 297 CYPSQTNFVLIDFKRPADELFQALLEKGYIVRSGNALGF-PTSLRITIGTKEQNEEILAI 355 +P+ NFVL++ A E + L+E+ IVR + + LRI++GT+E+N++++ Sbjct: 286 IHPTHANFVLVEVP-AAKETYDHLIEQQIIVRDRSKVVLCDQCLRISVGTREENDQLIGK 344 Query: 356 LAEIL 360 L+E + Sbjct: 345 LSEFI 349 Lambda K H 0.317 0.134 0.382 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 342 Number of extensions: 24 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 360 Length of database: 354 Length adjustment: 29 Effective length of query: 331 Effective length of database: 325 Effective search space: 107575 Effective search space used: 107575 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory